<html>\r
-<head><title>Menus</title></head>\r
+<head><title>Alignment Window Menus</title></head>\r
\r
<body>\r
-<p><strong>Alignment Menu</strong></p>\r
+<p><strong>Alignment Window Menus</strong></p>\r
<ul>\r
<li><strong>File</strong></li>\r
<ul>\r
<a href="../io/index.html">alignment format</a> to save as.<br>\r
</em></li>\r
<li><strong>Export</strong> <em><br>\r
- Creates an alignment output maintaining the alignment background colours\r
- and group colours. If the alignment is wrapped, the output will also be\r
- wrapped and will have the same visible residue width as the open alignment.\r
+ Creates an alignment graphic with the current annotation,\r
+ alignment background colours and group colours. If the alignment is <a\r
+ href="../features/wrap.html">wrapped</a>, the output will also\r
+ be wrapped and will have the same visible residue width as the\r
+ open alignment. \r
</em>\r
<ul>\r
<li><strong>HTML<br>\r
<li><strong>CLUSTAL</strong></li>\r
<li><strong>BLC</strong></li>\r
<li><strong>PIR</strong></li>\r
- <li><strong>PFAM<br>\r
- </strong></li>\r
+ <li><strong>PFAM</strong><br></li>\r
</ul>\r
</li>\r
<li><strong>Print<br>\r
your alignment window width, whichever is the smaller. <br>\r
</em></li>\r
<li><strong>Load Associated Tree<br>\r
- </strong><em>Jalview can load in trees which are in the Newick file format\r
- and associate them with a particular alignment. Note: the ids of the tree\r
- file and your alignment MUST be the same.<br>\r
+ </strong><em>Jalview can <a\r
+ href="../calculations/treeviewer.html">view trees</a> stored in\r
+ the Newick file format, and associate them with the\r
+ alignment. Note: the ids of the tree file and your alignment\r
+ MUST be the same.<br>\r
</em></li>\r
<li><strong>Close<br>\r
- </strong><em>Close the alignment window. Be aware that changes to your alignment\r
- will not be save unless specifically actioned from the "Save As"\r
- menu.<br>\r
+ </strong><em>Close the alignment window. Make sure you have\r
+ saved your alignment before you close - either as a Jalview\r
+ project or by using the <strong>Save As</strong> menu.<br>\r
</em></li>\r
</ul>\r
<li><strong>Edit</strong></li>\r
<li><strong>Undo</strong><em><br>\r
This will undo any edits you make to the alignment. This applies to insertion\r
or deletion of gaps, cutting residues or sequences from the alignment or\r
- pasting sequences to the current alignment or sorting the alignment. It\r
- DOES NOT undo colour changes or adjustments to group sizes affect the annotation\r
- panel. <br>\r
+ pasting sequences to the current alignment or sorting the\r
+ alignment. <strong>NOTE:</strong> It DOES NOT undo colour\r
+ changes, adjustments to group sizes, or changes to the annotation panel. <br>\r
</em></li>\r
<li><strong>Redo<br>\r
</strong><em>Any actions which you undo can be redone using redo. <br>\r
Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.<br>\r
</em></li>\r
<li><strong>Copy</strong><br>\r
- <em>Copies the currently selected residues to the system clipboard. The\r
- format of copied residues is NAME<tab>START_RES<tab>END_RES<tab>SEQUENCE\r
- <br>\r
- Use <CTRL> and C (<APPLE> and C on MacOSX) to copy.<br>\r
+ <em>Copies the currently selected residues to the system\r
+ clipboard - you can also do this by pressing <CTRL> and C\r
+ (<APPLE> and C on MacOSX). <br>\r
+ If you try to paste the clipboard contents to a text editor, you will see\r
+ the format of the copied residues is a tab separated list:<br>\r
+<pre>\r
+NAME START_RES END_RES SEQUENCE\r
+</pre><br>\r
</em></li>\r
<li><strong>Paste </strong>\r
<ul>\r
</ul>\r
</li>\r
<li><strong>Delete<br>\r
- </strong><em>This will delete the currently selected residues without making\r
- a copy of them first.<br>\r
+ </strong><em>This will delete the currently selected residues\r
+ without copying them to the clipboard. Like the other edit\r
+ operations, this can be undone with <strong>Undo</strong>.<br>\r
</em></li>\r
<li><strong>Select All<br>\r
</strong><em>Selects all the sequences and residues in the alignment. <br>\r
selection. <br>\r
</em><strong> </strong></li>\r
<li><strong>Undefine Groups<br>\r
- </strong><em>The alignment will be reset with no defined groups. WARNING:\r
+ </strong><em>The alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:\r
This cannot be undone.<br>\r
</em></li>\r
<li><strong>Remove Left<br>\r
or select "Deselect All" to deselect all columns.<br>\r
</em></li>\r
<li><strong>Remove Empty Columns<br>\r
- </strong><em>All columns which contain purely gap characters ("-",\r
+ </strong><em>All columns which only contain gap characters ("-",\r
".") will be deleted.<br>\r
You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
</em><em><br>\r
</em></li>\r
<li><strong>Remove All Gaps</strong><br>\r
- <em>All gap characters ("-", ".") will be deleted from\r
+ <em><strong>All</strong> gap characters ("-", ".") will be deleted from\r
the alignment.<br>\r
You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
<br>\r
</em> </li>\r
<li><strong>Remove Redundancy<br>\r
</strong><em>Selecting this option brings up a window asking you to select\r
- a threshold. If the percentage identity between two sequences exceeds this\r
- value one of the sequences (the shorter) is discarded. Press the "Apply"\r
- button to remove redundant sequences.<br>\r
+ a threshold. If the percentage identity between any two sequences\r
+ (under the current alignment) exceeds this\r
+ value then one of the sequences (the shorter) is discarded. Press the "Apply"\r
+ button to remove redundant sequences. The "Undo" button will undo the last\r
+ redundancy deletion.<br>\r
</em></li>\r
<li><strong>Pad Gaps<br>\r
- </strong><em>If the sequences in an alignment window are not all the same\r
- length they can all be set to the length of the longest sequence by selecting\r
- "Pad Gaps." Any sequences which are shorter than the longest sequence\r
- in an alignment will have gap characters ("-" or ".")\r
- appended to the beginning or end to make them equal length. <br>\r
+ </strong><em>Adds gaps to the end of all the sequences so they\r
+ are all the same length. This is useful for making a tree using\r
+ unaligned sequences.<br>\r
You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
</em></li>\r
</ul>\r
<blockquote>\r
<ul>\r
<li><strong>Font<br>\r
- </strong><em>Change the font of the display. The default font can be set\r
- from the "Choose Font" window, which is shown when the "Font\r
- Menu" is selected. <br>\r
+ </strong><em>Change the font of the display from the\r
+ "Choose Font" dialog box, which is shown when this\r
+ item is selected. <br>\r
</em></li>\r
<li><strong>Wrap<br>\r
- </strong><em>The default alignment display shows sequences in a single horizontal\r
- row. If your alignment has only a few sequences you may wish to "Wrap"\r
- the alignment so that the sequences are shown on multiple horizontal rows.\r
+ </strong><em>When ticked, the alignment display is\r
+ "<a href="../features/wrap.html">wrapped</a>" to the\r
+ width of the alignment window. This is useful if your alignment\r
+ has only a few sequences to view its full width at once.<br>\r
Options are available to show the residue numbering at the start and/or\r
end of an alignment as well as showing the alignment position above each\r
sequence row. <br>\r
- NOTE: In the current version the wrap alignment should be used for viewing,\r
- not editing. <br>\r
+ <strong>NOTE</strong>: When in wrapped alignment view, the\r
+ alignment cannot be edited or have regions selected on it. <br>\r
</em><strong> </strong></li>\r
<li><strong>Show Full Sequence ID<br>\r
</strong><em>If this box is selected the sequence name will have the start\r
<li><strong>Colour Text<br>\r
</strong><em>If this is selected the residues will be coloured according\r
to the background colour associated with that residue. The colour is slightly\r
- darker than background to enable the residue to be read. <br>\r
+ darker than background so the amino acid symbol remains visible. <br>\r
</em></li>\r
<li><strong>Show Gaps<br>\r
- </strong><em>If this is selected gap characters will be displayed as "."\r
- or "-". If unselected gap characters will appear as blank spaces.\r
+ </strong><em>When this is selected, gap characters will be displayed as "."\r
+ or "-". If unselected, then gap characters will appear as blank spaces.\r
<br>\r
You may set the default gap character in <a href="../features/preferences.html">preferences</a>.<br>\r
</em></li>\r
</li>\r
<li><strong>Sequence Features<br>\r
</strong><em>If the sequence names are Swissprot entries Jalview will use\r
- the names to retrieve sequence features from the EBI. Features which are\r
+ the names to retrieve <a href="../features/seqfeatures.html">sequence features</a> from the EBI. Features which are\r
1 residue in length are coloured red, sequences longer than 1 residue are\r
coloured blue. Move the mouse over a coloured feature to display the details\r
of the feature. <br>\r
Note: The retrieved information will update the sequence start and end labels\r
if they are incorrect. <br>\r
</em></li>\r
- <li><strong>Overview Window<br>\r
+ <li><strong><a href="../features/overview.html">Overview Window</a><br>\r
</strong><em>A scaled version of the alignment will be displayed in a small\r
window. A red box will indicate the currently visible area of the alignment.\r
Move the visible region using the mouse. </em><strong> </strong></li>\r
</strong><em>If this is selected, any changes made to the background colour\r
will be applied to all currently defined groups.<br>\r
</em></li>\r
- <li><strong>None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor,\r
+ <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor,\r
Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried\r
Index, Nucleotide, User Defined<br>\r
</strong> <em>See <a href="../colourSchemes/index.html">colours</a> for\r
</li>\r
<li><strong>Modify Conservation Threshold<br>\r
</strong><em>Use this to display the conservation threshold slider window.\r
- Useful if the window has been closed. </em></li>\r
+ Useful if the window has been closed, or if the 'by\r
+ conservation' option appears to be doing nothing!</em><br></li>\r
<li><strong>Above Identity Threshold<br>\r
</strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage\r
Identity</a></em><strong>.<br>\r
at the top. </em><strong><br>\r
</strong></li>\r
</ul>\r
+ <em>The <a href="../calculations/sorting.html">Sort menu</a> will\r
+ have some additional options if you have just done a multiple\r
+ alignment calculation, or opened a tree viewer window.</em><br>\r
</li>\r
<li><strong>Calculate Tree </strong>\r
+ <br><em>Functions for calculating trees on the alignment or the\r
+ currently selected region. See <a\r
+ href="../calculations/tree.html">calculating trees</a>.</em>\r
<ul>\r
<li><strong>Average Distance Using % Identity</strong></li>\r
<li><strong>Neighbour Joining Using % Identity</strong></li>\r
<li><strong>Average Distance Using Blosum62</strong></li>\r
- <li><strong>Neighbour Joining Using Blosum62<br>\r
- </strong><em>See <a href="../calculations/tree.html">calculating trees</a>.</em><strong>\r
- <br>\r
- </strong></li>\r
+ <li><strong>Neighbour Joining Using Blosum62<br></strong></li>\r
</ul>\r
</li>\r
<li><strong>Pairwise Alignments</strong><br>\r
- <em>See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>\r
+ <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>\r
</li>\r
<li><strong>Principal Component Analysis</strong><br>\r
- <em>See <a href="../calculations/pca.html">Principal Component Analysis</a>.</em>\r
+ <em>Shows a spatial clustering of the sequences based on the\r
+ BLOSUM62 scores in the alignment. See <a href="../calculations/pca.html">Principal Component Analysis</a>.</em>\r
<br>\r
</li>\r
- <li><strong>Web Service <br>\r
+ <li><strong>Web Service<br>\r
</strong>\r
- <ul>\r
- <em>Selecting one of the following menu items will start a remote service\r
- on the high powered computing facility at the University of Dundee. You\r
- will need a continuous network connection in order to use these services.\r
+ <em>Selecting one of the following menu items starts a remote service\r
+ on compute facilities at the University of Dundee. You need a\r
+ continuous network connection in order to use these services\r
+ through Jalview.\r
</em>\r
- <li><strong>Clustal Alignment</strong></li>\r
- <li><strong>Clustal Realign</strong></li>\r
- <li><strong>JPred</strong></li>\r
- <li><strong>Muscle Alignment</strong></li>\r
- </ul>\r
+ <ul>\r
+ <li><strong>Clustal Alignment</strong><br><em>\r
+ Submits all, or just the currently selected sequences for alignment with clustal W.</em><br></li>\r
+ <li><strong>Clustal Realign</strong><br><em>\r
+ Submits the alignment or currently selected region for\r
+ re-alignment with clustal W. Use this if you have added some\r
+ new sequences to an existing alignment.</em><br></li>\r
+ <li><strong>Muscle Alignment</strong><br><em>\r
+ Submits all, or jut the currently selected sequences for\r
+ alignment using Muscle. Do not use this if you are working with\r
+ nucleic acid sequences.</em><br>\r
+ <li><strong>JPred</strong><br><em>\r
+ Secondary structure prediction by network consensus. The\r
+ behaviour of this calculation depends on the current selection:\r
+ <ul>\r
+ <li>If nothing is selected, and the displayed sequences appear to\r
+ be aligned, then a JNet prediction will be run for the first\r
+ sequence in the alignment, using the current\r
+ alignment. Otherwise the first sequence will be submitted for prediction.\r
+ </li>\r
+ <li>If\r
+ just one sequence (or a region on one sequence) has been selected,\r
+ it will be submitted to the automatic JNet prediction server\r
+ for homolog detection and prediction.\r
+ </li>\r
+<li>If a set of sequences are selected, and they appear to be aligned,\r
+then the alignment will be used for a Jnet prediction on the\r
+<strong>first</strong> sequence selected in the set (that is, the one\r
+that was first clicked on).\r
+</li>\r
+ \r
+</ul>\r
</li>\r
</ul>\r
<p> </p>\r
git://source.jalview.org / jalview.git / blobdiff